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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bioseq__info__task_2fetch_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/pubseq_gateway/cassandra/bioseq_info_task/fetch.cpp Source File

69

"date_changed,

hash

, gi, length, mol, sat, "

70

"sat_key, seq_ids, seq_state,

state

, tax_id, name, writetime(sat_key)

FROM

";

77  const string

& keyspace,

84

m_ConsumeCallback(std::move(consume_callback))

96  "CCassBioseqInfoTaskFetch: DataReadyCB can't be assigned " 97  "after the loading process has started"

);

109  static const string

s_Where_1 =

".bioseq_info WHERE accession = ?"

;

110  static const string

s_Where_2 = s_Where_1 +

" AND version = ?"

;

111  static const string

s_Where_3 = s_Where_2 +

" AND seq_id_type = ?"

;

112  static const string

s_Where_4 = s_Where_3 +

" AND gi = ?"

;

121  sql

.append(s_Where_4);

128  sql

.append(s_Where_3);

134  sql

.append(s_Where_2);

139  sql

.append(s_Where_1);

177  bool

acceptable =

true

;

236  for

(

auto const

& seq_id : target.

GetSeqIds

()) {

237

seq_id_types.

insert

(get<0>(seq_id));

240  for

(

auto const

& seq_id :

source

.GetSeqIds()) {

241  if

(seq_id_types.count(get<0>(seq_id)) == 0) {

276  bool

final_state =

true

;

282

final_state =

false

;

297

}

else if

(restarted) {

337

snprintf(

msg

,

sizeof

(

msg

),

"Failed to fetch bioseq info (key=%s.%s.%d.%d) unexpected state (%d)"

,

339  static_cast<int>

(

version

),

static_cast<int>

(seq_id_type),

#define BEGIN_IDBLOB_SCOPE

function< void(vector< CBioseqInfoRecord > &&)> TBioseqInfoConsumeCallback

BEGIN_IDBLOB_SCOPE const int fnVersion

const string kSelectStatement

function< void(CRequestStatus::ECode status, int code, EDiagSev severity, const string &message)> TDataErrorCallback

CBioseqInfoRecord::TSeqIdType GetSeqIdType() const

CBioseqInfoRecord::TVersion GetVersion() const

CBioseqInfoRecord::TGI GetGI() const

bool HasField(EFields field) const

TSeqIdType GetSeqIdType() const

TVersion GetVersion() const

CBioseqInfoRecord & SetWritetime(TWritetime value)

CBioseqInfoRecord & SetDateChanged(TDateChanged value)

CBioseqInfoRecord & SetSat(TSat value)

CBioseqInfoRecord & SetName(TName value)

CBioseqInfoRecord & SetLength(TLength value)

CBioseqInfoRecord & SetTaxId(TTaxId value)

CBioseqInfoRecord & SetSeqIdType(TSeqIdType value)

CBioseqInfoRecord & SetSatKey(TSatKey value)

CBioseqInfoRecord & SetState(TState value)

CBioseqInfoRecord & SetGI(TGI value)

CBioseqInfoRecord & SetMol(TMol value)

CBioseqInfoRecord & SetSeqState(TSeqState value)

static const TState kStateAlive

CBioseqInfoRecord & SetVersion(TVersion value)

CBioseqInfoRecord & SetHash(THash value)

CBioseqInfoRecord & SetAccession(const TAccession &value)

void x_InitializeAliveRecordQuery()

bool m_InheritanceAllowed

@ eFetchAliveVersionStarted

void x_PopulateRecord(CBioseqInfoRecord &record) const

unsigned int m_RestartCounter

vector< CBioseqInfoRecord > m_Records

void AllowInheritance(bool value)

bool x_InheritanceRequired()

CBioseqInfoFetchRequest m_Request

void SetDataReadyCB(shared_ptr< CCassDataCallbackReceiver > callback)

TBioseqInfoConsumeCallback m_ConsumeCallback

void SetConsumeCallback(TBioseqInfoConsumeCallback callback)

set< size_t > m_InheritanceRequired

void x_MergeSeqIds(CBioseqInfoRecord &target, CBioseqInfoRecord const &source)

bool x_IsMatchingNewRecord(CBioseqInfoRecord const &old_record, CBioseqInfoRecord const &new_record)

bool x_IsMatchingRecord()

atomic< int32_t > m_State

string GetKeySpace() const

void SetDataReadyCB3(shared_ptr< CCassDataCallbackReceiver > datareadycb3)

TCassConsistency GetReadConsistency() const

void SetupQueryCB3(shared_ptr< CCassQuery > &query)

bool CheckReady(shared_ptr< CCassQuery > qry, unsigned int restart_counter, bool &need_repeat)

vector< SQueryRec > m_QueryArr

shared_ptr< CCassQuery > ProduceQuery() const

void Error(CRequestStatus::ECode status, int code, EDiagSev severity, const string &message)

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

@ eDiag_Error

Error message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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